[Bio-software] Re: Need help in running blastall through CGI

Joe Landman via bio-soft%40net.bio.net (by landman from scalableinformatics.com)
Sat Jul 21 13:20:52 EST 2007


Hi Ambarish

ambarish biswas wrote:
> Hi,
>     I'm trying to call "blastall" through a CGI script, but the database 
> option "-d nt" is not being available through CGI Scripts.I have 
> formated the nt.gz file properly and  I successfully executed the 
> blastall program from command line too but not from the CGI Script. The 
> .ncbirc file is also in place. Following is the error message of the 
> command " blastall -p blastn -d nt -i /tmp/CP000670.fna -o output.txt"

Could you show me how you formatted the nt database?

> 
> [blastall] WARNING: Unable to open nr.nin
> [blastall] WARNING: gi|145212960|gb|CP000670.1|: Unable to open nr.nin

This is usually an issue when either the BLASTDB entry in .ncbirc is 
incorrect, or you are missing the nt database (really, that the nt 
database has not been formatted)

> clearly its not finding the "blast/data" folder. To solve that problem i 
> have specified the "-d /home/user/blast/data/nt"
>  But then the error message appeared as below:
> 
> [blastall] WARNING: Unable to open nt.00.nin
> [blastall] WARNING: Unable to open nt.01.nin
> [blastall] WARNING: Unable to open nt.02.nin
> [blastall] WARNING: Unable to open nt.03.nin
> ...............................
> [blastall] WARNING: gi|145212960|gb|CP000670.1|: Unable to open nt.00.nin
> [blastall] WARNING: gi|145212960|gb|CP000670.1|: Unable to open nt.01.nin
> [blastall] WARNING: gi|145212960|gb|CP000670.1|: Unable to open nt.02.nin
> [blastall] WARNING: gi|145212960|gb|CP000670.1|: Unable to open nt.03.nin

Ok, this is a formatting issue. Could you show me all the steps that you 
used to format the database, including which directory you put them in?

> ......................
> 
> 
> I have tried all possible way, given the path in $PATH, also used $env 
> etc. But still couldn't fix the problem. So, need your help, i have kept 
> the blastall program in the /root/bin folder so its available 

Umm...  this is not a good idea.  You likely want blastall in /usr/bin, 
and you want it with 755 permissions

	cp /root/bin/blastall /usr/bin
	chmod 755 /usr/bin/blastall   # makes blastall rwxr-xr-x

> everywhere, only the problem is with the "/data" folder. can you please 
> suggest a way. I'm working with this problem so long and now its being 
> really hard on me.

If you use our rpms from 
http://downloads.scalableinformatics.com/downloads/ncbi/ you should have 
it installed in the right location (along with the scoring matrices). 
Then you need to construct your .ncbirc to look like

[NCBI]
Data=/usr/share/ncbi/data
[BLAST]
BLASTDB=/data/

make sure /data is world readable/writeable

	chmod 777 /data

and place your nt in /data , and format it

	cd /data
	formatdb -o T -v 1024 -p F nt

(use anything from 256 to 8192 as the argument to -v, it depends upon 
the amount of memory in your machine)

Joe

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Joseph Landman, Ph.D
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Scalable Informatics LLC,
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